As COVID-19 reaches a growing number of communities across Africa, governments’ efforts to contain the spread of the virus need to be accompanied by measures to minimize disruptions to the food system. To date, the emerging crisis is viewed primarily through a public health lens (as it should) and only gradually are national strategies, task forces and funds focusing attention on the spill-over economic and food security impacts. There are emerging signs of the negative impact of COVID-19 on the agrifood system, including difficulties in moving food from rural to urban areas, closed markets, rising food prices, loss of livelihoods, workers fleeing to rural areas and increased reliance on social safety nets. In some countries, these problems add to ongoing problems of locust/fall armyworm infestations or civil conflict. In many countries, COVID-19 will challenge structurally weak agrifood systems.